Workflow: 02-peakcall.cwl

Fetched 2021-11-29 21:41:09 GMT

DNase-seq 02 quantification

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Inputs

ID Type Title Doc
input_bam_format String

BAM or BAMPE for single-end and paired-end reads respectively (default: BAM)

input_bam_files File[]
nthreads Integer

Steps

ID Runs Label Doc
count-peaks
../utils/count-with-output-suffix.cwl (CommandLineTool)

Counts lines in a file and returns a suffixed file with that number

spp
../spp/spp.cwl (CommandLineTool)
peak-calling-narrow
../peak_calling/macs2-callpeak.cwl (CommandLineTool)
extract-peak-frag-length
../spp/extract-best-frag-length.cwl (CommandLineTool)

Extracts best fragment length from SPP output text file

filter-reads-in-peaks
../peak_calling/samtools-filter-in-bedfile.cwl (CommandLineTool)

Filter BAM file to only include reads overlapping with a BED file

count-reads-filtered
../peak_calling/count-reads-after-filtering.cwl (CommandLineTool)

Count number of dedup-ed reads used in peak calling

extract-count-reads-in-peaks
../peak_calling/samtools-extract-number-mapped-reads.cwl (CommandLineTool)

Extract mapped reads from BAM file using Samtools flagstat command

Outputs

ID Type Label Doc
output_read_in_peak_count_within_replicate File[]

Peak counts within replicate

output_narrowpeak_file File[]

peakshift/phantomPeak results file

output_extended_narrowpeak_file File[]

peakshift/phantomPeak extended fragment results file

output_peak_count_within_replicate File[]

Peak counts within replicate

output_peak_xls_file File[]

Peak calling report file (*_peaks.xls file produced by MACS2)

output_filtered_read_count_file File[]

Filtered read count reported by MACS2

output_spp_x_cross_corr File[]

peakshift/phantomPeak results file

output_spp_cross_corr_plot File[]

peakshift/phantomPeak results file

Permalink: https://w3id.org/cwl/view/git/1a0dd34d59ec983d1f7ad77bff35da2f016e3134/v1.0/DNase-seq_pipeline/02-peakcall.cwl